Difference between revisions of "Rizzo Lab Downloads"

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(Alternative Ligand Starting Geometries)
(SB2010 Docking Database [2010.05.19 Initial Release])
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|  Energy and Bump Grids
|  Energy and Bump Grids
|| To be released
|| [http://george.ams.sunysb.edu/SB2010/2010.09.13_grids.tar.gz 2010.09.13_grids.tar.gz]
== DOCK Input Files ==
== DOCK Input Files ==

Revision as of 15:39, 13 September 2010

SB2010 Docking Database [2010.05.19 Initial Release]

The base version of the database is presented as Receptors, Ligands and Spheres, which is applicable to any docking program. The spheres and grids are meant to be used with any version of the DOCK program. SB2010 is an on-going project; more structures and related resources will be added in the future.

Resource Filename
Receptors, Ligands and Spheres SB2010.05.19_rec.lig.sph.tar.gz
Energy and Bump Grids 2010.09.13_grids.tar.gz

DOCK Input Files

These are the DOCK input files used to evaluate the database.

Resource Filename
Rigid (RGD) RGD
Fixed Anchor (FAD) FAD
Flexible Ligand (FLX) FLX

SB2010 Ligand Flexibility Subsets

The Flexibility Subset Lists divide the database into three subsets to allow benchmarking of docking programs across three ligand flexibility ranges.

Resource Filename
7 or less 7orless
8 to 15 8to15
15+ 15+
All Systems all

SB2010 Protein Families [2010.05.19 Initial Release]

The 25 large protein families in the database are presented as subsets below. Another 25 smaller families (i.e less than 7 members) are also present in the database.

Protein Family Size
Factor Xa 41
Neuraminidase 43
Sialidase 11
Ribonuclease T1 7
OMP Decarboxylase 7
Estrogen Receptor 45
T4 Lysozyme 13
Beta Trypsin 29
Streptavidin 8
Thrombin 37
Tyrosine Phosphatase 20
HMG COA Reductase 20
Ribonuclease A 14
Alpha Trypsin 46
Acetylcholinesterase 19
HIV Protease 60
Thermolysin 26
Carboxypeptidase A 8
Matrix Metalloprotease 14
Egg Lysozyme 14
Phospholipase A2 15
Thymidylate Synthase 12
Carbonic Anhydrase 29

Aligned Families

Alignment for 5 protein families are presented. Each receptor was aligned to the first PDB code in the corresponding family list above. The same transformation was then applied to the ligand. Since energy and bump grids for the aligned receptors are also included, these files are fairly large (300MB-1.4GB).

Carbonic Anhydrase

HIV Protease


Reverse Transcriptase


Sample Docking Results

Sample docking results with the top scored pose for each pdb code. These results were produced with DOCK 6.4, using the dock input files shown above. Please note that you will get slightly different results, depending on the environment you use to compile the dock binaries.

Sample Docked Poses

Alternative Ligand Starting Geometries

XXXX.lig.mmff94x_gasmin.mol2 are alternative initial ligand coordinates obtained from gas-phase minimization (in absence of the receptor) with the MMFF94x forcefield with the MOE 2009.10 program. MMFF94x charges are assigned to the ligands before minimization.

MMFF94x Ligands

Starting geometries optimized with gaff, opls, am1 and pm3mm were generated as well. These are available on request.


This database is derived from structures originally downloaded from the Protein Data Bank. This resource is meant to be freely useably by the docking community, both academic and commercial institutions. The manuscript for this work has been submitted and is currently under review.

Contact Information

Please contact Sudipto.email.png if you face any problems.